Align galactaro-1,5-lactonase (characterized)
to candidate AZOBR_RS22710 AZOBR_RS22710 gluconolactonase
Query= reanno::WCS417:GFF3393 (291 letters) >FitnessBrowser__azobra:AZOBR_RS22710 Length = 296 Score = 271 bits (692), Expect = 2e-77 Identities = 138/285 (48%), Positives = 171/285 (60%), Gaps = 5/285 (1%) Query: 8 DARNAVGECPVWVPGENALYWVDIPKGGLQRWSAATGHVAAWTAPQMLACIARTDAGNWV 67 D RN GE PVW + W+DIP + R ++G WT P+M+ + G V Sbjct: 8 DLRNGTGENPVWDAERGSWTWIDIPARTIHRLDPSSGAHRRWTLPEMIGSLVLRPDGGVV 67 Query: 68 AGMETGFFQLT-PHNDGSLDTTLLAAVEHPRQDMRLNDGRCDRQGRFWAGSMVLNMGLNA 126 ETG F + P G T LA P++ MR NDGRCDRQGRFW SMV+++ Sbjct: 68 CACETGVFDVDLPGEGGEAVVTALATHRFPKEGMRFNDGRCDRQGRFWLSSMVMDISKGD 127 Query: 127 AEGTLYRYT-SGAAPHAQLDGFITLNGLAFSPDGRTMYASDSHPLVQQIWAFDYDIDTGT 185 + G +R+T + G+I NG AFSPDGRT+YASDSH V+ +WA+DYD DTGT Sbjct: 128 SSGLWHRFTRADGLTETGTGGYIIPNGSAFSPDGRTLYASDSHRDVRMVWAWDYDTDTGT 187 Query: 186 PSNRRVFVDMHKHLGRPDGAAVDADGCYWICANDAGLIHRFSPDGRLDRSLTVPVKKPTM 245 NRR FVDM +GRPDGAAVD DGCYWIC D G I RF+P+G LDR + VP++KPTM Sbjct: 188 ADNRRPFVDMRAMVGRPDGAAVDIDGCYWICCLDEGCIKRFTPNGDLDRRIEVPMRKPTM 247 Query: 246 CAFGGSRLDTLFVTSIR---DDQSEQSLSGGVFALNPGVVGLPEP 287 CAFGG L T+ VTS+ D +E G V +PG GLPEP Sbjct: 248 CAFGGPDLRTMLVTSLSRGPADLAEDPHGGRVLMFDPGAQGLPEP 292 Lambda K H 0.321 0.137 0.443 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 423 Number of extensions: 32 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 291 Length of database: 296 Length adjustment: 26 Effective length of query: 265 Effective length of database: 270 Effective search space: 71550 Effective search space used: 71550 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory